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Abstract: SA-OR48

Single-Cell Resolution Regulatory Landscape of the Kidney Highlights Cellular Differentiation Programs and Renal Disease Targets

Session Information

Category: Development, Stem Cells, and Regenerative Medicine

  • 500 Development, Stem Cells, and Regenerative Medicine

Authors

  • Miao, Zhen, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Balzer, Michael S., University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Ma, Ziyuan, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Liu, Hongbo, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Wu, Junnan, University of Pennsylvania, Philadelphia, Pennsylvania, United States
  • Susztak, Katalin, University of Pennsylvania, Philadelphia, Pennsylvania, United States

Group or Team Name

  • Susztak Lab
Background

The kidney cells undergo complex differentiation during development, among which the nephron progenitors differentiate to more than 10 different epithelial cells. However, the driver pathways, cell type specific transcription factors and regulatory circuits are not fully understood.

Methods

Here we conducted single-nucleus ATAC sequencing (snATAC-seq) and single cell RNA-sequencing (scRNA-seq) of kidneys from developing and adult mice. After quality control, we obtained 66,254 scRNA-seq and 28,316 snATAC-seq profiles.

Results

Through clustering analysis, we identified all major cell types in the kidney. By integrating snATAC-seq and scRNA-seq data, we revealed cell type- and developmental stage-specific cis-regulatory elements and inferred promoter-enhancer regulatory units. We defined key cell identity TFs and their gene targets through co-expression patterns.
To study cell-type specification of renal epithelial cells, we conducted trajectory analysis and resolved the developmental pseudotime along cell differentiation from nephron progenitors. We show that early differentiation of podocytes from the nephron progenitor pool is associated with sustained Foxl1 expression. Differentiation of renal tubule cells followed a more complex pattern, where Hfn4a expression is associated with a more proximal fate, while Tfap2b is coupled to the distal tubule differentiation. After cell specification, terminal differentiation was strongly linked to metabolic nuclear receptors such as Essra and Ppara for proximal tubules and Esrrb and Ppargc1a in loop of Henle.
We also implemented snATAC-seq data to leverage our understanding of human kidney disease development. By overlapping the chromatin landscape with kidney disease GWAS signals, we inferred key cell types for GWAS loci in the proximity of Shroom3 and Dab2 genes. Interestingly, we observed that some kidney disease-associated loci, such as those in the vicinity of Uncx, are only accessible in the developing kidney cells, indicating a developmental stage regulatory role of genetic variants.

Conclusion

Here we present a comprehensive open chromatin and gene expression landscape for developing mouse kidney and illustrate the use of single-cell multi-omics data to study gene regulatory dynamics and its relationship to complex human disease genetics.

Funding

  • NIDDK Support